Have you fully paid for the work? If not, get your builder back, and express your dis-satisfaction with the finish, but it does rather depend what your initial agreement was.
Personnally I have never cut skirting to fit flooring, prefering to remove and refit.
In all honesty if you didn't want beading the solution was to remove skirting, lay floor and replace skirting - but that would probably mean redecoration afterwards unless they were very careful.
If you are dissatisfied with the work don't pay them until they have corrected it. If you have paid still get them back in. If the bottom edge of the skirting is that damaged it should be replaced at THEIR expense because they failed to do a job properly that you paid for.
Having said that UMHO they must have been nuts to take on the job if the spec was to trim the bottom of the skirts "in situ". It was bound to end in tears.
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